Architecturally, the mosque is largely inspired by Ottoman cannons. It reproduces the plan of the great imperial mosques like the Blue Mosque, from which it is largely inspired. Thus, the Muhammad Ali mosque borrows from it the square courtyard – or sahn – open to the sky and bordered by arcades and the cascade of domes and half-domes. The prayer room is a quadrangular unit articulated around the central dome, reaching a height of 52 metres and a diameter of 21 metres. It is supported by a series of four half-cupolas, which are supplemented by four smaller cupolas at each of the corners of the sanctuary. All are decorated inside with paintings and gilding, while the walls of the mosque incorporate high alabaster panels rising to more than 11 metres. That is why the sanctuary is sometimes called the “alabaster mosque”.

The mosque contains the marble tomb of Muhammad Ali, located in the south-eastern part of the shrine. It is encircled by a bronze door made in the late 19th century. The bulging mihrab is surmounted by a half-dome. The mosque also has the distinction of having two minbars, one in gilded cedar wood and the other in alabaster, made at the request of King Farouk.

Muhammad Ali chose to build his state mosque entirely in the architectural style of his former overlords, the Ottomans, unlike the Mamluks who, despite their political submission to the Ottomans, stuck to the architectural styles of the previous Mamluk dynasties.

The mosque was built with a central dome surrounded by four small and four semi-circular domes. It was constructed in a square plan and measured 41×41 meters. The central dome is 21 meters in diameter and the height of the building is 52 meters. Two elegant cylindrical minarets of Turkish type with two balconies and conical caps are situated on the western side of the mosque, and rise to 82 meters.

The use of this style, combined with the presence of two minarets and multiple half-domes surrounding the central dome — features reserved for mosques built on the authority of the Sultan — were a defiant declaration of de facto Egyptian independence.

The main material is limestone but the lower storey and forecourt is tiled with alabaster up to 11,3 meters. The external facades are severe and angular and rise about four storeys until the level of the lead-covered domes.

The mihrab on the south-eastern wall is three storeys high and covered with a semi-circular dome. There are two arcades on the second storey, rising on columns and covered with domes. Although there are three entrances on each side of the forecourt, the usual entry is through the north-eastern gate. The forecourt measures 50×50 meters. It is enclosed by arched riwaks rising on pillars and covered by domes.

There is a brass clock tower in the middle of the north-western riwak, which was presented to Muhammad Ali by King Louis Philippe of France in 1845. The clock was reciprocated with the obelisk of Luxor now standing in Place de la Concorde in Paris.

The interior has a measure of 41×41 meters and gives a great feeling of space. The use of two levels of domes gives a much greater sense of space than there actually is. The central dome rises on four arches standing on colossal piers. There are four semicircular domes around the central dome. There are four smaller domes on the corners as well. The domes are painted and embellished with motifs in relief. The walls and pillars are covered with alabaster up to 11 meters high.